chr19-48575967-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_177973.2(SULT2B1):c.98G>A(p.Arg33Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00363 in 1,613,454 control chromosomes in the GnomAD database, including 113 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_177973.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SULT2B1 | NM_177973.2 | c.98G>A | p.Arg33Gln | missense_variant | 2/7 | ENST00000201586.7 | |
SULT2B1 | NM_004605.2 | c.53G>A | p.Arg18Gln | missense_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SULT2B1 | ENST00000201586.7 | c.98G>A | p.Arg33Gln | missense_variant | 2/7 | 1 | NM_177973.2 | P2 | |
SULT2B1 | ENST00000323090.4 | c.53G>A | p.Arg18Gln | missense_variant | 1/6 | 1 | A2 | ||
ENST00000666424.1 | n.493+20779C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00420 AC: 639AN: 152042Hom.: 23 Cov.: 30
GnomAD3 exomes AF: 0.00761 AC: 1893AN: 248884Hom.: 64 AF XY: 0.00724 AC XY: 975AN XY: 134732
GnomAD4 exome AF: 0.00357 AC: 5223AN: 1461296Hom.: 90 Cov.: 30 AF XY: 0.00350 AC XY: 2545AN XY: 726902
GnomAD4 genome ? AF: 0.00420 AC: 639AN: 152158Hom.: 23 Cov.: 30 AF XY: 0.00471 AC XY: 350AN XY: 74386
ClinVar
Submissions by phenotype
SULT2B1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 22, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Sep 01, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at